Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate 351618 BT2090 methylmalonyl-CoA mutase large subunit (NCBI ptt file)
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__Btheta:351618 Length = 715 Score = 905 bits (2339), Expect = 0.0 Identities = 461/716 (64%), Positives = 555/716 (77%), Gaps = 9/716 (1%) Query: 7 FDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAG 66 F ++D+ A PA+ A E G W T E I V ++ ++ + M+ L AG Sbjct: 5 FKNLDIYAAFQPANGA----EWQKANGISADWNTPEHIDVKPVYTKEDLEGMEHLGYAAG 60 Query: 67 IPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYD 126 +PP++ GPY+ MY RPWTIRQYAGFSTA+ESNAFYRRNLA+GQKGLSVAFDL THRGYD Sbjct: 61 LPPYLRGPYSVMYTLRPWTIRQYAGFSTAEESNAFYRRNLASGQKGLSVAFDLATHRGYD 120 Query: 127 SDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQG 186 D+ RV GDVG AGV+I S+ +M+ LF GIPL +MSVSMTMNGAVLPI+A Y+ EQG Sbjct: 121 PDHERVVGDVGKAGVSICSLENMKVLFDGIPLSKMSVSMTMNGAVLPIMAFYINAGLEQG 180 Query: 187 VKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQ 246 K E++AGTIQNDILKEFMVRNTYIYPP SM+IIS+IF YTS MPK+NSISISGYHMQ Sbjct: 181 AKLEEMAGTIQNDILKEFMVRNTYIYPPAFSMKIISDIFEYTSQKMPKFNSISISGYHMQ 240 Query: 247 EAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARM 306 EAGATADIE+AYTLADG++Y+RAG + G+++D FAPRLSFFW IG N FME+AK+RAARM Sbjct: 241 EAGATADIELAYTLADGLEYLRAGTAAGIDIDAFAPRLSFFWAIGTNHFMEIAKMRAARM 300 Query: 307 LWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTN 366 LWAK+V QF PKNPKS++LRTHSQTSGWSLT QD +NNV RTCIEAMAA GHTQSLHTN Sbjct: 301 LWAKIVKQFNPKNPKSLALRTHSQTSGWSLTEQDPFNNVGRTCIEAMAAALGHTQSLHTN 360 Query: 367 SLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQE 426 +LDEAIALPTDFSARIARNTQ+++Q+E+ + +DPW GS YVE LT +LA KAW I+E Sbjct: 361 ALDEAIALPTDFSARIARNTQIYIQEETYICKNVDPWGGSYYVEALTNELAHKAWERIEE 420 Query: 427 VEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNS 486 VEK+GGMAKAIE GIPKMRIEEAAARTQARIDSG Q ++GVNKYRLE E P+D+L++DN+ Sbjct: 421 VEKLGGMAKAIETGIPKMRIEEAAARTQARIDSGSQTIVGVNKYRLEKEAPIDILEIDNT 480 Query: 487 TVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVG 546 V EQ L +L+ R+ +V AL IT + NLL+L ++A R AT+G Sbjct: 481 AVRLEQIENLKRLKEGRNQAEVDKALAAITECV-----ETGKGNLLELAVEAARVRATLG 535 Query: 547 EMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMG 606 E+S A EKV GRY A IRTISGVYS E KN + + A EL E+F + EGR+PRI++AKMG Sbjct: 536 EISYACEKVVGRYKAIIRTISGVYSSESKNDGDFKRACELAEKFAKKEGRQPRIMVAKMG 595 Query: 607 QDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVP 666 QDGHDRG KV+AT YAD GFDVD+GPLFQTP E AR+AVE DVHVVGVSSLA GH TL+P Sbjct: 596 QDGHDRGAKVVATGYADCGFDVDMGPLFQTPAEAAREAVENDVHVVGVSSLAAGHKTLIP 655 Query: 667 ALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKL 722 + +EL KLGR DI++ GGVIP QD+D L K G I+ PGT + ++A +++ L Sbjct: 656 QIMEELKKLGREDIVVIAGGVIPAQDYDFLYKAGVAAIFGPGTPVAKAACQILEIL 711 Lambda K H 0.317 0.133 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1384 Number of extensions: 51 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 728 Length of database: 715 Length adjustment: 40 Effective length of query: 688 Effective length of database: 675 Effective search space: 464400 Effective search space used: 464400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory